Here is the answer to this question: Web Templates and FastCGI/Proxy Cache | Hestia Control Panel
Correct, you can change those php directives in that file or create a new php-fpm template and use it for your site (it is explained in above link).
Yes, the files you add as WEBSERVER.ssl.conf_WHATEVER and WEBSERVER.conf_WHATEVER won’t be overrided when rebuilding your user or site.
Cheers,
sahsanu